Introduction ~~~~~~~~ Anvio is an analysis and visualization platform for 'omics data.
- 7.0
Commands ~~~~~~~ - anvi-analyze-synteny - anvi-cluster-contigs - anvi-compute-ani - anvi-compute-completeness - anvi-compute-functional-enrichment - anvi-compute-gene-cluster-homogeneity - anvi-compute-genome-similarity - anvi-convert-trnaseq-database - anvi-db-info - anvi-delete-collection - anvi-delete-hmms - anvi-delete-misc-data - anvi-delete-state - anvi-dereplicate-genomes - anvi-display-contigs-stats - anvi-display-metabolism - anvi-display-pan - anvi-display-structure - anvi-estimate-genome-completeness - anvi-estimate-genome-taxonomy - anvi-estimate-metabolism - anvi-estimate-scg-taxonomy - anvi-estimate-trna-taxonomy - anvi-experimental-organization - anvi-export-collection - anvi-export-contigs - anvi-export-functions - anvi-export-gene-calls - anvi-export-gene-coverage-and-detection - anvi-export-items-order - anvi-export-locus - anvi-export-misc-data - anvi-export-splits-and-coverages - anvi-export-splits-taxonomy - anvi-export-state - anvi-export-structures - anvi-export-table - anvi-gen-contigs-database - anvi-gen-fixation-index-matrix - anvi-gen-gene-consensus-sequences - anvi-gen-gene-level-stats-databases - anvi-gen-genomes-storage - anvi-gen-network - anvi-gen-phylogenomic-tree - anvi-gen-structure-database - anvi-gen-variability-matrix - anvi-gen-variability-network - anvi-gen-variability-profile - anvi-get-aa-counts - anvi-get-codon-frequencies - anvi-get-enriched-functions-per-pan-group - anvi-get-sequences-for-gene-calls - anvi-get-sequences-for-gene-clusters - anvi-get-sequences-for-hmm-hits - anvi-get-short-reads-from-bam - anvi-get-short-reads-mapping-to-a-gene - anvi-get-split-coverages - anvi-help - anvi-import-collection - anvi-import-functions - anvi-import-items-order - anvi-import-misc-data - anvi-import-state - anvi-import-taxonomy-for-genes - anvi-import-taxonomy-for-layers - anvi-init-bam - anvi-inspect - anvi-interactive - anvi-matrix-to-newick - anvi-mcg-classifier - anvi-merge - anvi-merge-bins - anvi-meta-pan-genome - anvi-migrate - anvi-oligotype-linkmers - anvi-pan-genome - anvi-profile - anvi-push - anvi-refine - anvi-rename-bins - anvi-report-linkmers - anvi-run-hmms - anvi-run-interacdome - anvi-run-kegg-kofams - anvi-run-ncbi-cogs - anvi-run-pfams - anvi-run-scg-taxonomy - anvi-run-trna-taxonomy - anvi-run-workflow - anvi-scan-trnas - anvi-script-add-default-collection - anvi-script-augustus-output-to-external-gene-calls - anvi-script-calculate-pn-ps-ratio - anvi-script-checkm-tree-to-interactive - anvi-script-compute-ani-for-fasta - anvi-script-enrichment-stats - anvi-script-estimate-genome-size - anvi-script-filter-fasta-by-blast - anvi-script-fix-homopolymer-indels - anvi-script-gen-CPR-classifier - anvi-script-gen-distribution-of-genes-in-a-bin - anvi-script-gen-help-pages - anvi-script-gen-hmm-hits-matrix-across-genomes - anvi-script-gen-programs-network - anvi-script-gen-programs-vignette - anvi-script-gen-pseudo-paired-reads-from-fastq - anvi-script-gen-scg-domain-classifier - anvi-script-gen-short-reads - anvi-script-gen_stats_for_single_copy_genes.R - anvi-script-gen_stats_for_single_copy_genes.py - anvi-script-gen_stats_for_single_copy_genes.sh - anvi-script-get-collection-info - anvi-script-get-coverage-from-bam - anvi-script-get-hmm-hits-per-gene-call - anvi-script-get-primer-matches - anvi-script-merge-collections - anvi-script-pfam-accessions-to-hmms-directory - anvi-script-predict-CPR-genomes - anvi-script-process-genbank - anvi-script-process-genbank-metadata - anvi-script-reformat-fasta - anvi-script-run-eggnog-mapper - anvi-script-snvs-to-interactive - anvi-script-tabulate - anvi-script-transpose-matrix - anvi-script-variability-to-vcf - anvi-script-visualize-split-coverages - anvi-search-functions - anvi-self-test - anvi-setup-interacdome - anvi-setup-kegg-kofams - anvi-setup-ncbi-cogs - anvi-setup-pdb-database - anvi-setup-pfams - anvi-setup-scg-taxonomy - anvi-setup-trna-taxonomy - anvi-show-collections-and-bins - anvi-show-misc-data - anvi-split - anvi-summarize - anvi-trnaseq - anvi-update-db-description - anvi-update-structure-database - anvi-upgrade
You can load the modules by:
module load biocontainers
module load anvioExample job ~~~~~ .. warning:: Using #!/bin/sh -l as shebang in the slurm job script will cause the failure of some biocontainer modules. Please use #!/bin/bash instead.
To run Anvio on our our clusters:
#!/bin/bash
#SBATCH -A myallocation # Allocation name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 8
#SBATCH --job-name=anvio
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out
module --force purge
ml biocontainers anvio
anvi-script-reformat-fasta assembly.fa -o contigs.fa -l 1000 --simplify-names --seq-type NT
anvi-gen-contigs-database -f contigs.fa -o contigs.db -n 'An example contigs database' --num-threads 8
anvi-display-contigs-stats contigs.db
anvi-setup-ncbi-cogs --cog-data-dir $PWD --num-threads 8 --just-do-it --reset
anvi-run-ncbi-cogs -c contigs.db --cog-data-dir COG20 --num-threads 8